Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,793,557	C→T	37.2%	N141N (AAC→AAT)	gabP →	gamma‑aminobutyrate transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,793,557	0	C	T	37.2%	28.8 / 29.2	51	N141N (AAC→AAT)	gabP	gamma‑aminobutyrate transporter
Reads supporting (aligned to +/- strand): ref base C (26/6); new base T (11/8); total (37/14)
Fisher's exact test for biased strand distribution p-value = 1.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATCC  >  minE/1793507‑1793624

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:3358737/1‑69 (MQ=255)

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:3338497/1‑69 (MQ=255)

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:1431249/1‑69 (MQ=255)

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:1500965/1‑69 (MQ=255)

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:2751937/1‑69 (MQ=255)

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:2584576/1‑69 (MQ=255)

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:2463978/1‑69 (MQ=255)

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:2318302/1‑69 (MQ=255)

cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                                   >  1:1734435/1‑69 (MQ=255)

      tGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACgg                                              >  1:3047236/1‑68 (MQ=255)

           aTTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTaaa                                                      >  1:1724588/1‑55 (MQ=255)

               tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGa                                     >  1:1241837/1‑68 (MQ=255)

               tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGa                                     >  1:2270643/1‑68 (MQ=255)

               tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAg                                    >  1:1419960/1‑69 (MQ=255)

               tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAg                                    >  1:569431/1‑69 (MQ=255)

               tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAg                                    >  1:1788878/1‑69 (MQ=255)

               tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAg                                    >  1:2542712/1‑69 (MQ=255)

                          tACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCtggctggc                         <  1:1667118/69‑1 (MQ=255)

                           aCCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGgcg                        >  1:1836693/1‑69 (MQ=255)

                                cGCCTTAACCGG‑AGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt                  <  1:644270/69‑2 (MQ=255)

                                 gCCTTAATCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg                   >  1:3101452/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAAt                                         >  1:1069886/1‑46 (MQ=38)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTTGCTGGCGCtgtg                   >  1:2821661/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtttg                   >  1:211517/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg                   >  1:353485/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg                   >  1:517412/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg                   >  1:554738/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg                   >  1:1595027/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg                   >  1:2554604/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg                   >  1:2268817/1‑68 (MQ=255)

                                 gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg                   >  1:200746/1‑68 (MQ=255)

                                   cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt                  <  1:2551474/67‑2 (MQ=255)

                                   cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt                  <  1:1633996/67‑2 (MQ=255)

                                   cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt                  <  1:2906187/67‑2 (MQ=255)

                                   cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt                  <  1:204256/67‑2 (MQ=255)

                                   cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt                  <  1:3102761/67‑2 (MQ=255)

                                   cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt                  <  1:1970320/67‑2 (MQ=255)

                                        cTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTc            <  1:2661793/68‑1 (MQ=255)

                                            cAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt                  <  1:2306432/58‑2 (MQ=255)

                                              gTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTa     <  1:2077188/69‑1 (MQ=255)

                                              gTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTGCTGGCTGGCGCTGTGCAAAGTCATCGCTa     <  1:1993000/69‑1 (MQ=255)

                                               tAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTa     <  1:2237463/68‑1 (MQ=255)

                                               tAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTAt    <  1:3271089/69‑1 (MQ=255)

                                                aaCTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTAt    >  1:1262105/1‑68 (MQ=255)

                                                aaCTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATc   >  1:738081/1‑69 (MQ=255)

                                                aaCTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATc   >  1:3338930/1‑69 (MQ=255)

                                                aaCTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATc   >  1:322433/1‑69 (MQ=255)

                                                aaCTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATc   >  1:2645748/1‑69 (MQ=255)

                                                 aCTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATcc  >  1:428372/1‑69 (MQ=255)

                                                 aCTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATcc  >  1:1560035/1‑69 (MQ=255)

                                                 aCTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATcc  >  1:1887967/1‑69 (MQ=255)

CCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTCATCGCTATCC  >  minE/1793507‑1793624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A